[Bioperl-l] GenBank ASN.1 SeqIO parser
golharam at umdnj.edu
Thu Feb 7 18:00:33 EST 2008
That I can use from Perl? Such as????
I need to retrieve Gene Ontology information (classification and GO id)
from the Entrez Gene record. I thought it would be easiest using
BioPerl to do this. BioPerl only has an ASN.1 parser, entrezgene.
When I use this to load the Gene record, I'm using:
my $io = Bio::SeqIO->new(-file => '</tmp/gene.asn', -format =>
my $seq_obj = $io->next_seq;
Something is not working with the second line. I get an error:
"Use of uninitialized value in string eq at
It sort of makes sense because, well, the Entrez Gene record doesn't
have a sequence...it has information about a gene.
I figure I must be doing something wrong but I haven't seen anything in
BioPerl about parsing entrez gene records any other way.
Jason Stajich wrote:
> ugh - why parse ASN.1? NCBI provides converter application in the ncbi
> toolkit to many formats : genbank, XML, etc.
> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote:
>> No. The only ASN.1 parser is entrezgene. You could probably try
>> building one using the same ASN.1 parser that SeqIO::entrezgene uses
>> (Bio::ASN1::EntrezGene); it includes a parser for sequences:
>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote:
>>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought
>>> it would have been genbank or entrezgene, but neither of them work.
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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